Add tests for load_trajectory

Author: dwhswenson

paths_cli/tests/commands/test_load_trajectory.py

@@ -0,0 +1,83 @@
+from click.testing import CliRunner
+from contextlib import contextmanager
+import pytest
+from importlib import resources
+from openpathsampling.tests.test_helpers import data_filename
+import openpathsampling as paths
+
+from paths_cli.commands.load_trajectory import *
+
+
+@contextmanager
+def run_load_trajectory(args):
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        storage = paths.Storage("setup.nc", 'w')
+        storage.close()
+        results = runner.invoke(
+            load_trajectory,
+            args
+        )
+        assert results.exit_code == 0
+        st = paths.Storage("setup.nc", mode='r')
+        assert len(st.trajectories) == 1
+        yield st
+
+
+@pytest.mark.parametrize("with_top", [True, False])
+@pytest.mark.parametrize("with_tag", [True, False])
+def test_load_trajectory_pdb(with_top, with_tag):
+    # test that we can load a PDB file with or without topology; also tests
+    # that the taging works correctly
+    pdb_path = data_filename("ala_small_traj.pdb")
+    out_file = "setup.nc"
+    args = [
+        pdb_path,
+        '--append-file', out_file,
+    ]
+    if with_top:
+        args.extend(['--top', pdb_path])
+
+    if with_tag:
+        args.extend(['--tag', 'init_snap'])
+
+    with run_load_trajectory(args) as st:
+        traj = st.trajectories[0]
+        assert len(traj) == 10
+        if with_tag:
+            tagged = st.tags['init_snap']
+            assert tagged == traj
+
+def test_load_trajectory_trr():
+    trr = data_filename("gromacs_engine/project_trr/0000000.trr")
+    gro = data_filename("gromacs_engine/conf.gro")
+    out_file = "setup.nc"
+    args = [
+        trr,
+        '--append-file', out_file,
+        '--top', gro,
+    ]
+    with run_load_trajectory(args) as st:
+        traj = st.trajectories[0]
+        assert len(traj) == 4
+
+def test_load_trajectory_bad_topology():
+    trr = data_filename("gromacs_engine/project_trr/0000000.trr")
+    pdb = data_filename("tip4p_water.pdb")
+    out_file = "setup.nc"
+    args = [
+        trr,
+        '--append-file', out_file,
+        '--top', pdb,
+    ]
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        storage = paths.Storage("setup.nc", 'w')
+        storage.close()
+        result = runner.invoke(
+            load_trajectory,
+            args
+        )
+        assert result.exit_code == 1
+        assert "topology" in str(result.exception)
+        assert "same atoms" in str(result.exception)